“Outbreak”, “pandemic”, “quarantine”, “curfew”. Not so long ago, these words referred to a sci-fi blockbuster, or a distant past event – such as the Spanish Flu pandemic of 1920. Today, we all have experienced what is the global impact of the emergence of a new, highly contagious pathogen. Although mechanisms and thorough planning of mitigation measures have been developed for a theoretical scenario, through the current pandemic, it became evident that the development of effective and efficient, robust, accurate, and portable detection systems are of utmost significance.
The STAMINA Project counts ten months of work-in-progress. The “Bio-Partners” of STAMINA have been busy, putting all their effort, knowledge and expertise into the development of point-of-care tools, aiming to deliver a system for the early detection of pathogens (viruses/bacteria). This work is comprised of three phases:
Phase 1: development of novel biomarkers for the detection of each pathogen investigated under the STAMINA Project
Phase 2: experimental validation of the biomarkers and development of functional protocols using point-of-care (POC) devices
Phase 3: integration of the POC test results to the STAMINA engine
During phase 1, Bioinformatics took the lead to identify novel biomarkers for the detection of the pathogens under investigation, including SARS-CoV-2. The innovation and novelty of the tools developed in this phase represent a pivotal element for the progression of the work carried out downstream. During phase 1, thousands of genomes were stored, analyzed, and processed, allowing us to unravel and isolate key elements of the pathogens’ genetic code. Indeed, an important aspect to consider was the question “does this identified sequence actually work?”. The answer is based on deciphering and processing all the genetic data collected, utilizing novel computational/bioinformatics tools, and subsequently filtering and selecting the most prominent sequences. As expected, this step was rather demanding and valuable for the next phase. Based on these selected sequences, the mighty hero of bioinformatics once again transformed them into primers and probes. The latter underwent functionality assessment and validation in phase 2; from in silico, we moved rapidly to in vitro, where everything came to life. In this phase, the art of Molecular Biology took over, with the Bio-Partners giving their best; experimental planning, validation, optimization of protocols, evaluation of results, to name a few of the work steps carried out within this phase. After climbing step-by-step this ladder, the POC devices are ready to be tested.
But why is a POC device so important? The magic behind such devices lays in the fact that they are – by nature – miniaturised bench-top molecular analysers. However, despite their size, they tend to perform the same way compared to a bench-top – and sometimes even outperform. They are portable, light in weight, compact, while their results are accurate, reliable, repeatable. On top of that, they are all affordable prices. The reason for choosing a POC device instead of a regular bench-top when dealing with a potential outbreak is straightforward: it erases from the equation the logistics while it shortens the time from “sample collection” to “sample result”. Hence, an end-user gets the answer as fast as possible, and, as a result, can act accordingly.
In simple words, this work connects two fields of science: Bioinformatics and Molecular Biology. These key elements are united to create an interconnected point-of-care tool, meeting the needs of the end-users for portability, accuracy, fast detection and cost-efficiency. The POC devices make it possible for the end-users to break a strikeout of the regular bench-top laboratory equipment and move to the on-site “battlefield” of a potential pandemic.
All of the Bio-Partners in STAMINA are proud that their collaboration evolves and excels, while the technologies flourish!
